The correct link: http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919
Previous mail:
I am a non-programmer working on Prochlorococcus (a marine
bacteria) for which UCSC and Ensembl do not yet have
genome/transcriptome available or uploaded. Howe
Good Morning Noa:
Which one of the files at microbesonline are you trying to work with ?
--Hiram
- Original Message -
From: "Noa Sher"
To: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file
Hi Hiram,
I was trying to work with the tab delineated file (using the link
under export genomic data).
Thanks
noa
On 04/12/2011 20:29, Hiram Clawson wrote:
Good Morning Noa:
Which one of the files at microbesonline are you trying to work with ?
There are at least six of them there. Which one ?
- Original Message -
From: "Noa Sher"
To: "Hiram Clawson"
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf
fileissues
Hi Hi
Is this the genome you are working with:
http://archaea.ucsc.edu/cgi-bin/hgGateway?db=procMari_CCMP1375
- Original Message -
From: "Noa Sher"
To: "Hiram Clawson"
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong li
Pardon me, I see there is only one that says "tab-delimited" file.
That is a tough one to decode. It almost looks like GTF already, but
not quite. If we take it as a simple file of annotations on the genome,
without structure such as exons, introns, and merely rework the columns
to turn it into
Hi Hiram,
I managed to extract the columns in a different order (albeit I
did it in excel and not using command line) but then the 9th
column (attributes) of gtf is what I had problems with
Thanks
noa
On 04/12/2011 21:43, Hiram Clawson wrote:
For your full 9-column GTF file, it is, as you have determined, tab-delimited
for the 9 columns. In the ninth you can place any value tag pairs with
semi-colon ; delimiter. Beware your excel produced file does not have
hidden characters that can upset the balance. View your file in
an editor tha
Hi galaxy users,
Am I right in thinking there is no tool for sorting a sam/bam file in Galaxy?
I think this has probably been discussed before, sorry. I just want to
check I haven't missed anything, since sibling tools from e.g. the
samtools and picard suites are wrapped.
Thanks,
Clare
--
E: s
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